Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 55.68 kDa 
• Atom Count: 3558 
• Residue Count: 414 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

6M2V

Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA.

• DOI: 10.2210/pdb6M2V/pdb
• NDB: 6M2V

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-01 Released: 2021-01-13 
• Deposition Author(s): Abhishek, S., Nakarakanti, N.K., Deeksha, W., Rajakumara, E.
• Funding Organization(s): Department of Biotechnology (DBT, India), Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.276 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Literature

Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA.

Abhishek, S., Nakarakanti, N.K., Deeksha, W., Rajakumara, E.

(2021) Int J Biol Macromol 170: 514-522

• PubMed: 33359809 
• DOI: 10.1016/j.ijbiomac.2020.12.149
• Primary Citation of Related Structures:  
  6M2V


• PubMed Abstract: 
  

Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. Recently, UHRF1 has been found to contribute to de novo non-CpG methylation, however, whether UHRF1 could recognize non-mCpG is unknown. Here, we have demonstrated through calorimetric measurements that the UHRF1 SRA can recognize mCpH and fully-mCpHpG, types of non-mCpG. Our ITC binding studies endorse the preferential reading of hemi-mCpG by UHRF1 SRA and also show 6-fold weaker binding for fully-mCpG than hemi-mCpG. Despite presence of symmetrical (5-methyl cytosine) 5mCs, stoichiometry of 1:1 for UHRF1 SRA binding to fully-mCpG indicates that UHRF1 SRA may not form a stable complex with fully-mCpG DNA. Contrarily, UHRF1 SRA recognizes fully-mCpHpG with a stoichiometry of 2:1 protein to DNA duplex with binding affinity higher than fully-mCpG. Our crystal structure of UHRF1 SRA bound to fully-mCpHpG DNA reveals dual flip-out mechanism of 5mC recognition. Metadynamics studies corroborates with ITC data that UHRF1 SRA could not form a stable complex with fully-mCpG DNA. Altogether, this study demonstrates that UHRF1 SRA recognizes non-mCpG DNA and exhibits contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition.

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Organizational Affiliation: 

Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India. Electronic address: [e-mail].

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, B	212	Mus musculus	Mutation(s): 0  Gene Names: Uhrf1, Np95 EC: 2.3.2.27
Find proteins for Q8VDF2 (Mus musculus) Explore Q8VDF2  Go to UniProtKB:  Q8VDF2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')	C, D	13	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.276 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.897	α = 90
b = 74.829	β = 90
c = 141.505	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-03-01 
• Released Date: 2021-01-13 
Deposition Author(s): Abhishek, S., Nakarakanti, N.K., Deeksha, W., Rajakumara, E.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--
Science and Engineering Research Board (SERB)	India	--

Revision History 

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Database references